Evolutionary game theory
All the answers before are valid, but I'd like to propose an alteration of the haters gonna hate theme that came up so often.
Why do haters hate?
There's several evolutionary reasons why creating ingroups and outgroups is strategically useful.
Typically, you will want to be part of the largest group that can sustain a robust majority in your country. The larger the group, the more people have to share resources, which is bad. If the group is too small, it cannot dominate the remainder of the population, which too is evolutionary bad.
How you draw these groups is pretty arbitrary (of course, there might be particular strategic reasons to include or exclude your augmented individuals in the group). A large part of earth history consists of different people trying to spread their version of how populations should be particioned ("Yes, they are all immigrants, but those are black..."). And typically, once you've managed to partition the population, it's very hard to change the idea in the people's head.
See for instance that it was strategically useful [aka a netgain of material wealth for the oppressors] to build coalitions against Jewish people in earlier centuries, and religion was used as a divisor. Nowadays, there are not as many strategic resources available to expropriation, and the likelihood of shifting the narrative enough to make expropriation is negligible -- "hating Jews" is not as useful [to the non-Jewish partition] as it once was, yet some people are still doing it. Persistence.
It's strategically useful to discriminate against enhanced beings if
- they are a strategic factor: Either they control a lot of resources, or they could be very powerful (good fighters etc)
- Other dimensions to partition the populations are less relevant (for example there exists no big religion divide beforehand)
- Somehow, the narratives evolve
- Suddenly, the planet gets much richer, and therefore fighting for resources more valuable than before
- Some strategic people have foreseen long-term consequences of enhanced humans and therefore coordinate hate speech
Of course, there could be other ways in which your enhanced beings have alienated themselves. As in X-Men, a few bad individuals may ruin everyone's reputation. But for those cases, I point at the other answers.